Variant report

Variant	rs11833542
Chromosome Location	chr12:10368265-10368266
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:10364743-10368315	Hela-S3	cervix:	n/a	n/a
2	RUNX3	chr12:10368021-10368454	GM12878	blood:	n/a	chr12:10368276-10368285 chr12:10368276-10368285
3	POLR2A	chr12:10365925-10368484	K562	blood:	n/a	n/a
4	STAT1	chr12:10367268-10368793	Hela-S3	cervix:	n/a	chr12:10368140-10368151 chr12:10367475-10367482 chr12:10368218-10368230 chr12:10368358-10368366
5	JUND	chr12:10368255-10368388	K562	blood:	n/a	n/a
6	POLR2A	chr12:10364695-10368382	HUVEC	blood vessel:	n/a	n/a
7	RUNX3	chr12:10368071-10368472	GM12878	blood:	n/a	chr12:10368276-10368285 chr12:10368276-10368285
8	POLR2A	chr12:10364689-10371257	IMR90	lung:	n/a	n/a
9	POLR2A	chr12:10364722-10368331	Hela-S3	cervix:	n/a	n/a
10	TBL1XR1	chr12:10368167-10368342	K562	blood:	n/a	n/a
11	CHD1	chr12:10363939-10368549	IMR90	lung:	n/a	chr12:10365036-10365046 chr12:10365423-10365433
12	EP300	chr12:10368158-10368422	K562	blood:	n/a	n/a
13	STAT3	chr12:10367160-10368268	Hela-S3	cervix:	n/a	chr12:10367475-10367482 chr12:10368218-10368230

No.	Distal block	Cell Line	Cell type
1	chr12:10367004..10369055-chr12:10765454..10767041,2	K562	blood:
2	chr12:10363710..10369534-chr12:10376619..10381190,6	K562	blood:
3	chr12:10364222..10366094-chr12:10367394..10369564,2	K562	blood:
4	chr1:41329419..41329951-chr12:10367814..10368363,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000255958	TF binding region
ENSG00000134539	Chromatin interaction
ENSG00000111196	Chromatin interaction
ENSG00000139112	Chromatin interaction
ENSG00000229528	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs10845073	0.94[CHB][hapmap]
rs73058083	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898757	chr12:10229281-10614641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1054811	chr12:10350587-10440005	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11833542	GABARAPL1	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:10364600-10368400	Active TSS	Fetal Kidney	kidney
2	chr12:10364600-10368800	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr12:10365000-10368600	Active TSS	Left Ventricle	heart
4	chr12:10365200-10368600	Active TSS	Placenta	Placenta
5	chr12:10366600-10368400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr12:10366600-10370600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:10366800-10368400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr12:10366800-10368400	Flanking Active TSS	Brain Anterior Caudate	brain
9	chr12:10366800-10369000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr12:10366800-10371000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr12:10366800-10372600	Weak transcription	Gastric	stomach
12	chr12:10366800-10373000	Weak transcription	Esophagus	oesophagus
13	chr12:10366800-10386600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr12:10367000-10368400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:10367000-10368400	Enhancers	Fetal Heart	heart
16	chr12:10367000-10368400	Flanking Active TSS	Stomach Smooth Muscle	stomach
17	chr12:10367000-10368600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr12:10367000-10368600	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr12:10367000-10368800	Enhancers	Fetal Thymus	thymus
20	chr12:10367000-10369000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr12:10367000-10370600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr12:10367000-10371800	Weak transcription	Fetal Muscle Trunk	muscle
23	chr12:10367000-10372400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:10367200-10368400	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr12:10367200-10368400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:10367200-10368400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr12:10367200-10368400	Enhancers	Stomach Mucosa	stomach
28	chr12:10367200-10368800	Flanking Active TSS	Liver	Liver
29	chr12:10367200-10369000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr12:10367200-10370200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr12:10367400-10368400	Enhancers	H9 Cell Line	embryonic stem cell
32	chr12:10367400-10368400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr12:10367400-10368400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr12:10367400-10368400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
35	chr12:10367400-10368400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr12:10367400-10368400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr12:10367400-10368400	Enhancers	Primary T cells from cord blood	blood
38	chr12:10367400-10368400	Enhancers	Primary hematopoietic stem cells	blood
39	chr12:10367400-10368400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
40	chr12:10367400-10368400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr12:10367400-10368400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr12:10367400-10368400	Flanking Active TSS	Adipose Nuclei	Adipose
43	chr12:10367400-10368400	Flanking Active TSS	Brain Cingulate Gyrus	brain
44	chr12:10367400-10368400	Enhancers	Fetal Lung	lung
45	chr12:10367400-10368400	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr12:10367400-10368400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr12:10367400-10368400	Flanking Active TSS	Hela-S3	cervix
48	chr12:10367400-10368400	Active TSS	Monocytes-CD14+_RO01746	blood
49	chr12:10367400-10368400	Enhancers	NHEK	skin
50	chr12:10367400-10369000	Enhancers	Fetal Brain Male	brain

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